Bacteriophytochromes RpBphP2 and RpBphP3 from the photosynthetic bacterium Rhodopseudomonas palustris work in tandem to modulate synthesis of the light-harvesting complex LH4 in response to light. Although RpBphP2 and RpBphP3 share the same domain structure with 52% sequence identity, they demonstrate distinct photoconversion behaviors. RpBphP2 exhibits the ''classical'' phytochrome behavior of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states, whereas RpBphP3 exhibits novel photoconversion between Pr and a nearred (Pnr) light-absorbing states. We have determined the crystal structure at 2.2-Å resolution of the chromophore binding domains of RpBphP3, covalently bound with chromophore biliverdin IX␣. By combining structural and sequence analyses with site-directed mutagenesis, we identify key residues that directly modulate the photochemical properties of RpBphP3 and RpBphP2. Remarkably, we identify a region spanning residues 207-212 in RpBphP3, in which a single mutation, L207Y, causes this unusual bacteriophytochrome to revert to the classical phenotype that undergoes reversible photoconversion between the Pr and Pfr states. The reverse mutation, Y193L, in the corresponding region in RpBphP2 significantly diminishes the formation of the Pfr state. We propose that residues 207-212 and the spatially adjacent conserved residues, Asp-216 and Tyr-272, interact with the chromophore and form part of the interface between the chromophore binding domains and the PHY domain that modulates photoconversion.biliverdin ͉ red-light photoreceptor P hytochromes are photoreceptors found in plants, cyanobacteria, fungi, and nonphotosynthetic bacteria that regulate a range of physiological responses such as chlorophyll synthesis, seed germination, floral induction, and phototaxis by using light in the red/far-red region of the spectrum (1). Upon absorption of a photon in the appropriate wavelength range, their linear tetrapyrrole chromophores (bilins) switch between two stable, spectrally distinct, red-and far-red-light absorbing forms, denoted Pr and Pfr, respectively. In most phytochromes Pr is the dark-adapted, ground state; in others, it is Pfr. The primary photochemical event for the Pr/Pfr photoconversion in plant phytochromes (Phys) and bacteriophytochromes (Bphs) is believed to involve rapid 15Z anti to 15E anti (15Za/15Ea) isomerization of the C15AC16 double bond between rings C and D of the bilin chromophore. Isomerization is followed by slower transitions via several spectrally distinct intermediates (2-4) that are presumably accompanied by structural changes in the chromophore and the surrounding protein.A pair of Bphs from the photosynthetic bacterium Rhodopseudomonas palustris, denoted RpBphP2 and RpBphP3, was characterized that in tandem modulates synthesis of the LH4 light-harvesting complex (5). RpBphP2 and RpBphP3 share the same biliverdin IX␣ (BV) chromophore and the same domain structure, in which three N-terminal photosensory domains, PAS (Per-ARNT-Sim), GAF (cGMP phosphodies...